Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PAF1

Cell type

Cell type Class
Digestive tract
Cell type
DLD-1
Primary Tissue
Colon
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
Isolated from Large intestine; Colon
cell line
DLD-1
tissue
Large intestine; Colon
treatment
IAA for 6 hours
chip antibody
PAF1
geo_loc_name
missing
collection_date
missing

Sequenced DNA Library

library_name
GSM6721424
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-Rx experiments were performed as previously described (Li et al., 2021; Wang et al., 2021). Briefly, 1×10^7 human cells were spiked-in with 1-2×10^6 MEF cells and were fixed with 1% paraformaldehyde in PBS for 10 minutes, and quenched with 0.125 M glycine for 5 minutes. Fixed cells were used for nuclei isolation and were sheared using the Diagenode Bruptor Plus with the high-power mode for 25 cycles (sonication cycle: 30 seconds ON, 30 seconds OFF). The chromatin was immunoprecipitated with 5 μg individual antibodies and 15 μL of pre-blocked Protein A/G beads (Santa Cruz, Cat# sc-2003). After wash for three times with wash buffer (50 mM HEPES-KOH at pH 7.5, 300 mM LiCl, 1 mM EDTA, 1.0% NP-40, 0.7% Na-Deoxycholate), the captured DNA was eluted and reverse-crosslinked with 200 μL of elution buffer (50 mM Tris-HCl at pH 8.0, 10 mM EDTA, 1.0% SDS, 200 μg/mL proteinase K) by incubating at 55°C overnight. The DNA was purified by phenol-chloroform extraction and ethanol precipitation. library strategy: ChIP-seq-Rx Following HaloPROTAC3 treatment, cells were collected and lysed with Trizol reagent. Total RNA was extracted according to the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg38

Number of total reads
20407561
Reads aligned (%)
57.1
Duplicates removed (%)
24.0
Number of peaks
262 (qval < 1E-05)

hg19

Number of total reads
20407561
Reads aligned (%)
56.9
Duplicates removed (%)
24.1
Number of peaks
221 (qval < 1E-05)

Base call quality data from DBCLS SRA